MICROBIOME & METAGENOMICS

Microbiome studies determine which microorganisms are present in the analysed sample, the structure of the community they form and how it changes between experimental conditions, environments or sample groups. Depending on the project objective, the analysis may include targeted sequencing of taxonomic markers such as the 16S rRNA, the 18S rRNA gene or the ITS region, or comprehensive sequencing of all DNA present in the sample using a shotgun metagenomics approach. We offer solutions for analysing bacterial, archaeal and fungal microbiomes, as well as other eukaryotic microorganisms. We help select the appropriate marker, amplification region, sequencing technology, required data output and scope of bioinformatics analysis based on the sample type and study objective.

Choose the service you are interested in to learn about sample material requirements, available sequencing options and the possible scope of data analysis.

• Targeted Amplicon Sequencing, which includes:
  0116S rRNA - for studies aimed at analysing bacterial genomes. Specific regions can be amplified, with V3+V4 the most commonly selected combination. Regions V1 through V9 can be analysed. Full-length 16S sequencing, covering all regions from V1 to V9 in a single assay, is available using the PacBio platform.

  0218S rRNA - used primarily for high-resolution taxonomic studies of fungi. The key difference between 16S and 18S rRNA is that 16S rRNA is a component of the 30S subunit in prokaryotic ribosomes, whereas 18S rRNA is a component of the 40S subunit in eukaryotic ribosomes.

  03ITS - a region widely used to analyse fungal diversity in environmental samples. You can choose to analyse the ITS1 or ITS2 region, or the entire ITS1+ITS2 fragment.
• Shotgun metagenomic sequencing - provides information on the total genomic DNA of all organisms in the sample, avoiding the need to isolate and culture microorganisms or amplify target regions. This is crucial as it is believed that nearly 99% of all microorganisms cannot be cultured in the laboratory. Shotgun metagenomic sequencing not only provides information on each organism's taxonomic annotation, but also functional profiling, gene prediction and microbial interactions.

Which service should you choose?

Do you want to compare microbiome composition across multiple samples?

Choose Targeted Amplicon Sequencing. This targeted approach is designed to profile selected groups of microorganisms and compare community structure.

Are you analysing bacteria or archaea?

Choose 16S rRNA-based sequencing. You can analyse a selected variable region or sequence the full-length gene.

Are you analysing fungal communities?

Choose amplicon sequencing of the ITS region. Depending on the required resolution, the analysis may cover the ITS1 region, ITS2 region or the full ITS fragment.

Do you need more accurate taxonomic identification?

Consider Full-Length 16S rRNA Gene and ITS Amplicon Sequencing, which uses longer marker sequences and can improve the resolution of microorganism classification.

Do you also want to investigate the functional potential of the microbiome?

Choose Shotgun Metagenomic Sequencing. This method analyses all DNA present in the sample without limiting the study to a single taxonomic marker.

Amplicon sequencing or shotgun metagenomics?

Amplicon Sequencing - Amplicon sequencing is suitable when the main project objective is to determine the composition of a selected microorganism group and compare community diversity across samples. The method requires selection of an appropriate marker and amplification region. The results primarily provide a relative taxonomic profile, while functional analysis is limited or predictive.

Shotgun Metagenomic Sequencing - Shotgun metagenomics analyses all available DNA fractions in the sample without primers targeting a single marker. It provides a broader range of information, including taxonomic composition, genes, metabolic pathways and potential functional characteristics of the community. However, it requires a larger amount of data and more extensive bioinformatics analysis.

Plan your project

The appropriate method depends on the sample type, the group of microorganisms being studied, the expected taxonomic resolution and whether the project aims to analyse only community composition or also its functional potential.

Provide us with information about the sample material, number of samples, microbiome being studied and project objective, and we will help you select the appropriate marker, sequencing technology and scope of data analysis.

COMPLETE THE PROJECT SPECIFICATION → here

Not sure whether to choose amplicon-based sequencing or a shotgun metagenomics approach? Complete the available information and indicate that you need help planning the experiment.

BOOK A CONSULTATION → here